but what exactly needs to be done when doing a major modification depends on your operating limitations, as issued during certification... typical is 5 hrs back in Phase I...may or may not need to notify FAA..
It depends entirely on your operating limitations. There have been several changes over the last 15 years. Check the paragraph outlining modifications. They will tell you exactly how to comply.
read page 164, section 19 for sample verbage of what your operating limitations will contain... that establishes what you have to do when doing major modification.